overlapGenes: Calculates Genes that overlap the SV region

In VilainLab/Nanotator: Next generation structural variant annotation and classification

Calculates Genes that overlap the SV region

Description

Calculates Genes that overlap the SV region

Usage

overlapGenes(
  bed,
  chrom,
  startpos,
  endpos,
  svid,
  chrom2,
  SVTyp,
  bperrorindel = 3000,
  bperrorinvtrans = 50000
)

Arguments

bed	Text Bionano Bed file.
chrom	character SVmap chromosome.
startpos	numeric starting position of the breakpoints.
endpos	numeric end position of the breakpoints.
svid	numeric Structural variant identifier (Bionano generated).
chrom2	character SVmap chromosome number 2.
SVTyp	Character. Type of SV.
bperrorindel	Numeric. base pair error indel.
bperrorinvtrans	Numeric. base pair error invtranslocation.

Value

Data Frame. Contains the SVID,Gene name,strand information and percentage of SV covered.

Examples

smapName="GM24385_Ason_DLE1_VAP_trio5.smap"
smap = system.file("extdata", smapName, package="nanotatoR")
bedFile <- system.file("extdata", "HomoSapienGRCH19_lift37.bed", 
       package="nanotatoR")
bed<-buildrunBNBedFiles(bedFile,returnMethod="dataFrame")
smap<-readSMap_DLE(smap, input_fmt_smap = "Text")
chrom<-smap$RefcontigID1
chrom2 <- smap$RefcontigID2
startpos<-smap$RefStartPos
endpos<-smap$RefEndPos
if (length(grep("SVIndex",names(smap)))>0){
       svid <- smap$SVIndex
   }else{
    svid <- smap$SmapEntryID
    }
SVTyp <- smap$Type
overlapGenes(bed = bed, chrom = chrom, startpos = startpos, 
   endpos = endpos, chrom2 = chrom2, svid = svid,
   SVTyp = SVTyp, 
   bperrorindel = 3000, bperrorinvtrans = 50000)

VilainLab/Nanotator documentation built on Aug. 2, 2024, 8:45 p.m.